Visualizing OPUS binary files and DPT files in R
Adrianne Seiden
2025-10-08
Reading OPUS files
This code is modified from the original OPUSreader2 documentation vignettes/opusreader2_introduction.Rmd by Philip Baumann and Thomas Knecht. It reads OPUS binary files and extracts metadata and absorbance data, which can then be plotted.
Plots & Metadata
The main function, read_opus(), reads one or more OPUS
files and returns a nested list of class list_opusreader2.
Each list contains both the spectral data and metadata for each file.
The dsn argument is the data source name. It can be a
character vector of folder paths (to read files recursively) or specific
OPUS file paths. Start by testing the read_opus function on your
corrected spectra folder, and saving the output of the first file.
#load opusreader2 from github.com/spectral-cockpit
library(opusreader2)
#save the path to your corrected spectra
# # Mac path
# corr_spectra <- "/Users/adrianneseiden/Library/CloudStorage/Box-Box/Salk Institute Project/AKS Salk files/Adrianne_FTIRdata/Corrected_files" # nolint
# # Windows path
# corr_spectra <- "C:/Users/adria/Box/Box-Box/Salk Institute Project/AKS Salk files/Adrianne_FTIRdata/Corrected_files" # nolint
# # Relative path
# corr_spectra <- "../Adrianne_FTIRdata/Corrected_files"
#save the data from your corrected files as 'data_test'
data_test <- read_opus(dsn = corr_spectra)
#check the names of the list
names(data_test)
> [1] "DRIFTS_pot001_13Cwheat_wk0_root_250725_corr.0"
> [2] "DRIFTS_pot012_13Csoy_wk10_root_250827_corr.0"
> [3] "DRIFTS_pot029_13Cwheat_wk10_root_250827_corr.0"
> [4] "DRIFTS_pot029_13Cwheat_wk40_root_250827_corr.0"
> [5] "DRIFTS_pot030_13Csoy_wk10_root_250725_corr.0"
> [6] "DRIFTS_pot030_13Csoy_wk40_root_250827_corr.0"
> [7] "DRIFTS_pot032_13Cwheat_wk0_root_250725_corr.0"
> [8] "DRIFTS_pot047_13Crice_wk0_root_250725_corr.0"
> [9] "DRIFTS_pot050_13Csoy_wk0_root_250827_corr.0"
> [10] "DRIFTS_pot052_13CnoPlant_wk30_root_250919_corr.0"
> [11] "DRIFTS_pot052_13CnoPlant_wk40_root_250919_corr.0"
> [12] "DRIFTS_pot053_13Cwheat_wk10_root_250725_corr.0"
> [13] "DRIFTS_pot053_13Cwheat_wk40_root_250919_corr.0"
> [14] "DRIFTS_pot055_13Crice_wk10_root_250725_corr.0"
> [15] "DRIFTS_pot055_13Crice_wk40_root_250827_corr.0"
> [16] "DRIFTS_pot055qmark_13Crice_wk10_root_250725_corr.0"
> [17] "DRIFTS_pot056_12Csoy_wk10_root_250919_corr.0"
> [18] "DRIFTS_pot062_13Csoy_wk0_root_250725_corr.0"
> [19] "DRIFTS_pot079_13Crice_wk0_root_250725_corr.0"
> [20] "DRIFTS_pot080_13Csoy_wk10_root_250725_corr.0"
> [21] "DRIFTS_pot080_13Csoy_wk40_root_250919_corr.0"
> [22] "DRIFTS_pot086_12Csoy_wk0_root_250919_corr.0"
> [23] "DRIFTS_pot087_13Crice_wk10_root_250827_corr.0"
> [24] "DRIFTS_pot087_13Crice_wk40_root_250919_corr.0"
> [25] "DRIFTS_pot094_13Csoy_wk10_root_250725_corr.0"
> [26] "DRIFTS_pot094_13Csoy_wk10_soil_250630_corr.0"
> [27] "DRIFTS_pot094_13Csoy_wk40_root_250919_corr.0"
> [28] "DRIFTS_pot103_13Crice_wk0_root_recNMR_250725_corr.0"
> [29] "DRIFTS_pot103_13Crice_wk0_root_vial1_250725_corr.0"
> [30] "DRIFTS_pot103_13Crice_wk0_root_vial2_250725_corr.0"
> [31] "DRIFTS_pot103_13Crice_wk0_root_vial3_250725_corr.0"
> [32] "DRIFTS_pot107_12Crice_wk0_root_really13_250725_corr.0"
> [33] "DRIFTS_pot109_13Cwheat_wk40_root_250919_corr.0"
> [34] "DRIFTS_pot119_13Crice_wk10_root_250827_corr.0"
> [35] "DRIFTS_pot119_13Crice_wk40_root_250919_corr.0"
# define 'meas_1' as the first element of the 'data_test' list
meas_1 <- data_test[[1]]Next I defined a function, plotSpectrum, to plot the spectral data from a single sample (meas_1)
# data is a list containing OPUS file data, including absorbance and metadata.
plotSpectrum <- function(data) { # nolint: object_name_linter.
ab_data <- data$ab
if (!is.null(ab_data) &&
!is.null(ab_data$wavenumbers) && !is.null(ab_data$data) &&
is.numeric(ab_data$wavenumbers) && is.numeric(ab_data$data) &&
length(ab_data$wavenumbers) == length(ab_data$data) &&
all(is.finite(ab_data$wavenumbers)) && all(is.finite(ab_data$data))) {
plot(
ab_data$wavenumbers, ab_data$data, type = "l",
xlab = "Wavenumber (cm⁻¹)", ylab = "Absorbance",
main = data$basic_metadata$dsn_filename,
xlim = rev(range(ab_data$wavenumbers))
)
} else {
cat("Absorbance data not found or not valid in this file.\n")
str(ab_data)
}
}
plotSpectrum(meas_1)
I then defined the metadataTable function, to extract and display the a subset of the metadata stored in the data extracted by ‘read_opus’ in a table format.
To view all the available data categories, run ‘names(meas_1)’ in the console. To view the parameters within these categories use str(meas_1$category_name) where ‘category_name’ is ‘basic_metadata’, ‘optics’, etc.
The plotMetadata function combines the plot and table for a single spectrum.
plotMetadata <- function(data) { # nolint: object_name_linter.
plotSpectrum(data)
metadataTable(data)
}
plotMetadata(meas_1)
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot001_13Cwheat_wk0_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:18:39 GMT-7 |
| Max Y | 0.799607157707214 |
| Min Y | -0.0012896629050374 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56884765625 |
| Experiment (method) | SALK_soils_method.xpm |
Combined plot and table (folder)
The following for loop runs plotMetadata on each spectrum in the data_test list, which contains all the spectra in the folder. It will plot each spectrum and print its metadata below.
for (i in seq_along(data_test)) {
cat("#### Spectrum", i, ":", names(data_test)[i], "\n\n")
data_i <- data_test[[i]]
ab_data <- data_i$ab
valid <- !is.null(ab_data) &&
!is.null(ab_data$wavenumbers) && !is.null(ab_data$data) &&
is.numeric(ab_data$wavenumbers) && is.numeric(ab_data$data) &&
length(ab_data$wavenumbers) == length(ab_data$data) &&
all(is.finite(ab_data$wavenumbers)) && all(is.finite(ab_data$data))
if (valid) {
plotSpectrum(data_i)
print(metadataTable(data_i))
} else {
cat("Data not valid or missing for this spectrum.\n")
str(ab_data)
}
}Spectrum 1 : DRIFTS_pot001_13Cwheat_wk0_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot001_13Cwheat_wk0_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:18:39 GMT-7 |
| Max Y | 0.799607157707214 |
| Min Y | -0.0012896629050374 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56884765625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 2 : DRIFTS_pot012_13Csoy_wk10_root_250827_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot012_13Csoy_wk10_root_250827_corr.0 |
| Timestamp | 2025-08-27 18:52:52 GMT-7 |
| Max Y | 0.797225415706635 |
| Min Y | -0.00604866677895188 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.560791015625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 3 : DRIFTS_pot029_13Cwheat_wk10_root_250827_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot029_13Cwheat_wk10_root_250827_corr.0 |
| Timestamp | 2025-08-27 18:53:45 GMT-7 |
| Max Y | 0.722125887870789 |
| Min Y | -0.00508248526602983 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.559814453125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 4 : DRIFTS_pot029_13Cwheat_wk40_root_250827_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot029_13Cwheat_wk40_root_250827_corr.0 |
| Timestamp | 2025-08-27 18:54:46 GMT-7 |
| Max Y | 0.828895390033722 |
| Min Y | -0.00468211621046066 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.560791015625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 5 : DRIFTS_pot030_13Csoy_wk10_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot030_13Csoy_wk10_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:21:37 GMT-7 |
| Max Y | 0.84355878829956 |
| Min Y | -0.00326710939407349 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56689453125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 6 : DRIFTS_pot030_13Csoy_wk40_root_250827_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot030_13Csoy_wk40_root_250827_corr.0 |
| Timestamp | 2025-08-27 18:54:58 GMT-7 |
| Max Y | 0.721331775188446 |
| Min Y | -0.00639449199661613 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.559814453125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 7 : DRIFTS_pot032_13Cwheat_wk0_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot032_13Cwheat_wk0_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:22:45 GMT-7 |
| Max Y | 0.909599244594574 |
| Min Y | -0.00415003532543778 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56982421875 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 8 : DRIFTS_pot047_13Crice_wk0_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot047_13Crice_wk0_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:23:56 GMT-7 |
| Max Y | 0.712926685810089 |
| Min Y | -0.00133463030215353 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56591796875 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 9 : DRIFTS_pot050_13Csoy_wk0_root_250827_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot050_13Csoy_wk0_root_250827_corr.0 |
| Timestamp | 2025-08-27 18:55:10 GMT-7 |
| Max Y | 0.772085309028625 |
| Min Y | -0.00875790882855654 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.560791015625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 10 : DRIFTS_pot052_13CnoPlant_wk30_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot052_13CnoPlant_wk30_root_250919_corr.0 |
| Timestamp | 2025-09-19 18:16:15 GMT-7 |
| Max Y | 0.77551531791687 |
| Min Y | -0.005828230176121 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.392822265625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 11 : DRIFTS_pot052_13CnoPlant_wk40_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot052_13CnoPlant_wk40_root_250919_corr.0 |
| Timestamp | 2025-09-19 18:16:20 GMT-7 |
| Max Y | 0.813514113426208 |
| Min Y | -0.004625812638551 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.393798828125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 12 : DRIFTS_pot053_13Cwheat_wk10_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot053_13Cwheat_wk10_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:24:39 GMT-7 |
| Max Y | 0.997280716896057 |
| Min Y | -0.00962971057742834 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56591796875 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 13 : DRIFTS_pot053_13Cwheat_wk40_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot053_13Cwheat_wk40_root_250919_corr.0 |
| Timestamp | 2025-09-19 15:59:23 GMT-7 |
| Max Y | 0.797653913497925 |
| Min Y | -0.00369235360994935 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.389892578125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 14 : DRIFTS_pot055_13Crice_wk10_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot055_13Crice_wk10_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:26:35 GMT-7 |
| Max Y | 0.816974341869354 |
| Min Y | -0.00123318459372967 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56689453125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 15 : DRIFTS_pot055_13Crice_wk40_root_250827_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot055_13Crice_wk40_root_250827_corr.0 |
| Timestamp | 2025-08-27 18:55:22 GMT-7 |
| Max Y | 0.852853655815125 |
| Min Y | -0.00635257223621011 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56396484375 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 16 : DRIFTS_pot055qmark_13Crice_wk10_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot055qmark_13Crice_wk10_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:25:51 GMT-7 |
| Max Y | 0.907369911670685 |
| Min Y | -0.00234174402430654 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56591796875 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 17 : DRIFTS_pot056_12Csoy_wk10_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot056_12Csoy_wk10_root_250919_corr.0 |
| Timestamp | 2025-10-07 18:03:40 GMT-7 |
| Max Y | 0.615259230136871 |
| Min Y | -0.0116841280832887 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.393798828125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 18 : DRIFTS_pot062_13Csoy_wk0_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot062_13Csoy_wk0_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:27:28 GMT-7 |
| Max Y | 0.687717080116272 |
| Min Y | -0.00538174575194716 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56884765625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 19 : DRIFTS_pot079_13Crice_wk0_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot079_13Crice_wk0_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:28:00 GMT-7 |
| Max Y | 0.816869914531708 |
| Min Y | -0.00257659493945539 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56787109375 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 20 : DRIFTS_pot080_13Csoy_wk10_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot080_13Csoy_wk10_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:28:56 GMT-7 |
| Max Y | 0.77625048160553 |
| Min Y | -0.00814440380781889 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56689453125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 21 : DRIFTS_pot080_13Csoy_wk40_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot080_13Csoy_wk40_root_250919_corr.0 |
| Timestamp | 2025-09-19 16:42:23 GMT-7 |
| Max Y | 0.764196336269379 |
| Min Y | -0.00511131621897221 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.391845703125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 22 : DRIFTS_pot086_12Csoy_wk0_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot086_12Csoy_wk0_root_250919_corr.0 |
| Timestamp | 2025-10-07 18:04:00 GMT-7 |
| Max Y | 0.540434181690216 |
| Min Y | -0.0042975265532732 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.386962890625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 23 : DRIFTS_pot087_13Crice_wk10_root_250827_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot087_13Crice_wk10_root_250827_corr.0 |
| Timestamp | 2025-08-27 18:55:34 GMT-7 |
| Max Y | 0.699629366397858 |
| Min Y | -0.00116329535376281 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.560791015625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 24 : DRIFTS_pot087_13Crice_wk40_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot087_13Crice_wk40_root_250919_corr.0 |
| Timestamp | 2025-09-19 17:31:48 GMT-7 |
| Max Y | 0.879431128501892 |
| Min Y | -0.0040658856742084 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.392822265625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 25 : DRIFTS_pot094_13Csoy_wk10_root_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot094_13Csoy_wk10_root_250725_corr.0 |
| Timestamp | 2025-07-25 20:29:09 GMT-7 |
| Max Y | 1.27848649024963 |
| Min Y | -0.00875786785036325 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56689453125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 26 : DRIFTS_pot094_13Csoy_wk10_soil_250630_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot094_13Csoy_wk10_soil_250630_corr.0 |
| Timestamp | 2025-07-25 20:46:03 GMT-7 |
| Max Y | 0.821687042713165 |
| Min Y | -0.00153941253665835 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.454833984375 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 27 : DRIFTS_pot094_13Csoy_wk40_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot094_13Csoy_wk40_root_250919_corr.0 |
| Timestamp | 2025-09-19 16:42:30 GMT-7 |
| Max Y | 0.825236082077026 |
| Min Y | -0.00458295457065105 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.391845703125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 28 : DRIFTS_pot103_13Crice_wk0_root_recNMR_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot103_13Crice_wk0_root_recNMR_250725_corr.0 |
| Timestamp | 2025-07-25 20:30:32 GMT-7 |
| Max Y | 0.836920917034149 |
| Min Y | -0.00138377456460148 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56982421875 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 29 : DRIFTS_pot103_13Crice_wk0_root_vial1_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot103_13Crice_wk0_root_vial1_250725_corr.0 |
| Timestamp | 2025-07-25 20:30:55 GMT-7 |
| Max Y | 0.826825261116028 |
| Min Y | -0.000596170837525278 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56787109375 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 30 : DRIFTS_pot103_13Crice_wk0_root_vial2_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot103_13Crice_wk0_root_vial2_250725_corr.0 |
| Timestamp | 2025-07-25 20:31:26 GMT-7 |
| Max Y | 0.984898567199707 |
| Min Y | -0.00565983727574348 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56591796875 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 31 : DRIFTS_pot103_13Crice_wk0_root_vial3_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot103_13Crice_wk0_root_vial3_250725_corr.0 |
| Timestamp | 2025-07-25 20:31:46 GMT-7 |
| Max Y | 0.983739078044891 |
| Min Y | -0.0026757272426039 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56591796875 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 32 : DRIFTS_pot107_12Crice_wk0_root_really13_250725_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot107_12Crice_wk0_root_really13_250725_corr.0 |
| Timestamp | 2025-07-25 20:32:00 GMT-7 |
| Max Y | 1.03206670284271 |
| Min Y | -0.00172662467230111 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.56591796875 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 33 : DRIFTS_pot109_13Cwheat_wk40_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot109_13Cwheat_wk40_root_250919_corr.0 |
| Timestamp | 2025-09-19 15:59:28 GMT-7 |
| Max Y | 0.75251305103302 |
| Min Y | -0.00450036907568574 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.386962890625 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 34 : DRIFTS_pot119_13Crice_wk10_root_250827_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot119_13Crice_wk10_root_250827_corr.0 |
| Timestamp | 2025-08-27 18:55:49 GMT-7 |
| Max Y | 0.808935940265656 |
| Min Y | -0.0116460844874382 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.561767578125 |
| Experiment (method) | SALK_soils_method.xpm |
Spectrum 35 : DRIFTS_pot119_13Crice_wk40_root_250919_corr.0
| Parameter | Value |
|---|---|
| File Name | DRIFTS_pot119_13Crice_wk40_root_250919_corr.0 |
| Timestamp | 2025-09-19 17:31:43 GMT-7 |
| Max Y | 0.954932034015656 |
| Min Y | -0.00412484398111701 |
| Aperture Setting | 6 mm |
| Scanner Velocity | 10.0S |
| Result Spectrum | AB |
| Resolution | 4 |
| Sample Scans | 400 |
| End Frequency | 400 |
| Start Frequency | 4000 |
| Duration | 364.390869140625 |
| Experiment (method) | SALK_soils_method.xpm |
Stacking multiple spectra
Stacking re-runs
This code looks for files with the same sample number and stacks their spectra, to check whether reruns are consistent.
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
echo = TRUE,
results = "markup",
include = TRUE
)
library(opusreader2)
library(RColorBrewer)
data_test <- read_opus(dsn = corr_spectra)
# Helper to extract sample number from filename (e.g., "pot094")
extract_sample_number <- function(filename) {
m <- regexpr("[a-z]{3}[0-9]+", filename)
if (m[1] != -1) {
regmatches(filename, m)
} else {
NA
}
}
# Helper to extract sample type (e.g.,"soil", "root")
extract_sample_type <- function(filename) {
m <- regexpr("soil|root", filename, ignore.case = TRUE)
if (m[1] != -1) {
tolower(regmatches(filename, m))
} else {
NA
}
}
# Helper to extract timepoint (e.g., "wk0", "wk40")
extract_timepoint <- function(filename) {
m <- regexpr("wk[0-9]+", filename, ignore.case = TRUE)
if (m[1] != -1) {
tolower(regmatches(filename, m))
} else {
NA
}
}
# Group files by sample number, sample type, and timepoint
sample_numbers <- sapply(names(data_test), extract_sample_number)
sample_types <- sapply(names(data_test), extract_sample_type)
timepoints <- sapply(names(data_test), extract_timepoint)
# Create unique combinations of sample number, sample type, and timepoint
sample_combinations <- paste(sample_numbers, sample_types, timepoints, sep = "_")
unique_combinations <- unique(sample_combinations[!is.na(sample_numbers)
& !is.na(sample_types)
& !is.na(timepoints)])
# Plot stacked spectra for each unique combination
library(RColorBrewer)
for (combination in unique_combinations) {
idx <- which(sample_combinations == combination)
if (length(idx) > 1) {
# Extract sample number, type, and timepoint from combination
parts <- strsplit(combination, "_")[[1]]
sample_num <- parts[1]
sample_type <- parts[2]
timepoint <- parts[3]
spectra <- data_test[idx]
colors <- brewer.pal(min(length(spectra), 8), "Set1")
plot(NULL, xlim = rev(range(spectra[[1]]$ab$wavenumbers)),
ylim = range(sapply(spectra, function(x) x$ab$data), na.rm = TRUE),
xlab = "Wavenumber (cm⁻¹)", ylab = "Absorbance",
main = paste("Stacked spectra for", sample_num, "-", sample_type, "-", timepoint),
bty = "l")
for (i in seq_along(spectra)) {
ab_data <- spectra[[i]]$ab
if (!is.null(ab_data) && !is.null(ab_data$wavenumbers) &&
!is.null(ab_data$data)) {
lines(ab_data$wavenumbers, ab_data$data, col = colors[i], lwd = 2)
}
}
legend("topright",
inset = c(-0.05, -0.02),
legend = names(spectra),
col = colors[seq_along(spectra)],
lwd = 2,
xpd = TRUE,
bty = "n")
}
}
Stacking by crop & time
This code stacks spectra of the same crop and timepoint.
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
echo = TRUE,
results = "markup",
include = TRUE
)
# Helper functions to extract crop and timepoint from filename
extract_crop <- function(filename) {
m <- regexpr("rice|wheat|soy", filename, ignore.case = TRUE)
if (m[1] != -1) tolower(regmatches(filename, m)) else NA
}
extract_time <- function(filename) {
m <- regexpr("wk[0-9]+", filename, ignore.case = TRUE)
if (m[1] != -1) tolower(regmatches(filename, m)) else NA
}
extract_sample_type <- function(filename) {
m <- regexpr("root|soil", filename, ignore.case = TRUE)
if (m[1] != -1) {
tolower(regmatches(filename, m))
} else {
NA
}
}
# Get crop and time for each file
crops <- sapply(names(data_test), extract_crop)
times <- sapply(names(data_test), extract_time)
types <- sapply(names(data_test), extract_sample_type)
# Unique crop-time combinations
combos <- na.omit(unique(paste(crops, times, types, sep = "_")))
library(RColorBrewer)
for (combo in combos) {
idx <- which(paste(crops, times, types, sep = "_") == combo)
if (length(idx) > 1) {
spectra <- data_test[idx]
colors <- brewer.pal(min(length(spectra), 8), "Set1")
plot(NULL, xlim = rev(range(spectra[[1]]$ab$wavenumbers)),
ylim = range(sapply(spectra, function(x) x$ab$data), na.rm = TRUE),
xlab = "Wavenumber (cm⁻¹)", ylab = "Absorbance",
main = paste("Stacked spectra for", combo),
bty = "l")
for (i in seq_along(spectra)) {
ab_data <- spectra[[i]]$ab
if (!is.null(ab_data) &&
!is.null(ab_data$wavenumbers)
&& !is.null(ab_data$data)) {
lines(ab_data$wavenumbers, ab_data$data, col = colors[i], lwd = 2)
}
}
legend("topright",
inset = c(-0.05, -0.02),
legend = names(spectra),
col = colors[seq_along(spectra)],
lwd = 2,
xpd = TRUE,
bty = "n")
}
}
Reading DPT files
This code is modified from code by Stephany Soledad Chacon, “Box> Salk Institute Project> Salk Data> FTIR_Intact_decomposition_pots> FTIR_analysis.Rmd”. Using data in the DPT format, we can extrapolate sample attributes from the file names, then normalize and visualize spectra across replicates, crops, and timepoints. The width of the line bounding the spectra represents the range of the data.
Importing FTIR data using readr
Define file path and import multiple files into one data frame
#> Files found in directory:
#> [1] "DRIFTS_pot001_13Cwheat_wk0_root_250725.0.dpt"
#> [2] "DRIFTS_pot012_13Csoy_wk10_root_250827.0.dpt"
#> [3] "DRIFTS_pot029_13Cwheat_wk10_root_250827.0.dpt"
#> [4] "DRIFTS_pot029_13Cwheat_wk40_root_250827.3.dpt"
#> [5] "DRIFTS_pot030_13Csoy_wk10_root_250725.0.dpt"
#> [6] "DRIFTS_pot030_13Csoy_wk40_root_250827.0.dpt"
#> [7] "DRIFTS_pot032_13Cwheat_wk0_root_250725.0.dpt"
#> [8] "DRIFTS_pot047_13Crice_wk0_root_250725.0.dpt"
#> [9] "DRIFTS_pot050_13Csoy_wk0_root_250827.0.dpt"
#> [10] "DRIFTS_pot052_13CnoPlant_wk30_root_250919.0.dpt"
#> [11] "DRIFTS_pot052_13CnoPlant_wk40_root_250919.0.dpt"
#> [12] "DRIFTS_pot053_13Cwheat_wk10_root_250725.0.dpt"
#> [13] "DRIFTS_pot053_13Cwheat_wk40_root_250919.0.dpt"
#> [14] "DRIFTS_pot055_13Crice_wk10_root_250725.0.dpt"
#> [15] "DRIFTS_pot055_13Crice_wk10_root_qmark_250725.0.dpt"
#> [16] "DRIFTS_pot055_13Crice_wk40_root_250827.0.dpt"
#> [17] "DRIFTS_pot056_12Csoy_wk10_root_250919.0"
#> [18] "DRIFTS_pot062_13Csoy_wk0_root_250725.0.dpt"
#> [19] "DRIFTS_pot079_13Crice_wk0_root_250725.0.dpt"
#> [20] "DRIFTS_pot080_13Csoy_wk10_root_250725.0.dpt"
#> [21] "DRIFTS_pot080_13Csoy_wk40_root_250919.0.dpt"
#> [22] "DRIFTS_pot086_12Csoy_wk0_root_250919.0"
#> [23] "DRIFTS_pot087_13Crice_wk10_root_250827.0.dpt"
#> [24] "DRIFTS_pot087_13Crice_wk40_root_250919.0.dpt"
#> [25] "DRIFTS_pot094_13Csoy_wk10_root_250725.0.dpt"
#> [26] "DRIFTS_pot094_13Csoy_wk10_soil_250630.0.dpt"
#> [27] "DRIFTS_pot094_13Csoy_wk40_root_250919.0.dpt"
#> [28] "DRIFTS_pot103_13Crice_wk0_root_recNMR_250725.0.dpt"
#> [29] "DRIFTS_pot103_13Crice_wk0_root_vial1_250725.0.dpt"
#> [30] "DRIFTS_pot103_13Crice_wk0_root_vial2_250725.2.dpt"
#> [31] "DRIFTS_pot103_13Crice_wk0_root_vial3_250725.0.dpt"
#> [32] "DRIFTS_pot107_12Crice_wk0_root_really13_250725.0.dpt"
#> [33] "DRIFTS_pot109_13Cwheat_wk40_root_250919.0.dpt"
#> [34] "DRIFTS_pot119_13Crice_wk10_root_250827.0.dpt"
#> [35] "DRIFTS_pot119_13Crice_wk40_root_250919.0.dpt"
#> Number of .dpt files: 33Extract sample info from filename
Using the long format dataframe dpt_data format
example: DRIFTS_pot094_13Csoy_wk10_soil_250630.0.dpt
#> Column filenames: wavenumber absorbance filename
#> [1] "pot"
#> [1] "001" "012" "029" "030" "032" "047" "050" "052" "053" "055" "062" "080"
#> [13] "087" "094" "103" "107" "109" "119"
#> [1] 13 12
#> [1] "wheat" "soy" "rice" "noPlant"
#> [1] "wk0" "wk10" "wk40" "wk30"
#> [1] "root" "soil"
#> [1] "250725" "250827" "250919" "250630"
#> [1] NA "qmark" "vial2" "vial3" "really13"
#> # A tibble: 6 × 11
#> wavenumber absorbance filename source ID isotope crop timepoint type
#> <dbl> <dbl> <chr> <chr> <chr> <dbl> <chr> <chr> <chr>
#> 1 3998. 0.0115 DRIFTS_pot00… pot 001 13 wheat wk0 root
#> 2 3997. 0.0115 DRIFTS_pot00… pot 001 13 wheat wk0 root
#> 3 3995. 0.0115 DRIFTS_pot00… pot 001 13 wheat wk0 root
#> 4 3994. 0.0115 DRIFTS_pot00… pot 001 13 wheat wk0 root
#> 5 3993. 0.0115 DRIFTS_pot00… pot 001 13 wheat wk0 root
#> 6 3991. 0.0115 DRIFTS_pot00… pot 001 13 wheat wk0 root
#> # ℹ 2 more variables: run_date <chr>, notes <chr>Normalize absorbance data
For each file, create a normalized absorbance column (nabs) by dividing each absorbance value by the maximum absorbance for that file.
Plotting by timepoint and type
These plots are of normalized absorbance values. The thickness of the opaque line represents the range of the data. Dotted lines at specific wavenumbers indicate key absorption features.
Week 0
FALSE [1] "001" "032" "050" "062" "103" "107"Week 10
#> [1] "012" "029" "030" "053" "055" "080" "087" "119"
#> [1] "094"Week 40
#> [1] "029" "030" "052" "053" "055" "080" "087" "094" "109" "119"Plotting by crop
These plots are of normalized absorbance values. The thickness of the line represents the range of the data. Dotted lines at specific wavenumbers indicate key absorption features.
- 2900 cm-1 ← aliphatic (alkanes)
- 1730 - 1650 cm-1 ← carbonyl; C=O stretch (carbonyl, carboxylic acids, esters, ketones, etc.)
- 1500 cm-1 ← aromatic
I’m not sure if these are the best areas to highlight, but I kept what Stephany did.
Wheat Roots
#> [1] "001" "029" "032" "053" "109"rice roots
#> [1] "055" "087" "103" "107" "119"soy roots
#> [1] "012" "030" "050" "062" "080"